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HMMER
User's Guide
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Dept. of Genetics |
WashU |
Medical School |
Sequencing Center |
CGM |
IBC|
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Eddy lab |
Internal (lab only) |
HMMER |
PFAM |
tRNAscan-SE |
Software |
Publications
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Next: Plan 7
Up: Introduction
Previous: Profile HMMs
HMMER 2 is an almost complete rewrite of the original 1992-1996 HMMER
code. A list of the major changes follows.
- [Plan7] The model architecture is changed. The ``Plan 7''
architecture2.4 allows detailed control over parameters of local,
global, and multidomain alignments. In Plan 7, you choose the
alignment style when you build the model with hmmbuild, not
when you search. A single database search program hmmsearch
replaces the four search programs in HMMER 1.x.
- [Pfam support] There is much better support for the Pfam
HMM database. HMMs have names; the HMM file format allows libraries of
multiple HMMs per file; and there is a search program
hmmpfam
for searching a single query sequence against an HMM library.
HMM databases like Pfam can be indexed for rapid access using
hmmindex, and single HMMs can be retrieved from an HMM
database using hmmfetch.
- [E-values] HMMER now reports both log-odds scores and
a E-value. E-values can detect significant matches even when the
log-odds score is negative. A new program hmmcalibrate
empirically determines the necessary parameters for estimating
E-values as best as possible.
- [Output] Database searches now sort and postprocess their results for
prettier and more useful output. Output styles are deliberately
similar to BLAST, to try to simplify the design of postprocessors.
- [Save file format] HMMER save files are now in an ASCII format which
is easy for humans to read, portable across all architectures
without byteswapping issues, and compact.
- [Decent defaults] The ``best'' average behavior of HMMER is now its
default behavior. For example, mixture Dirichlet priors are now the
default for protein model building. In HMMER 1.x, you had to invoke a
number of ``experimental'' options to get better performance - this
led to a bunch of really frustrating benchmarking in the literature,
in which people compared fully optimized program X to the default
behavior of HMMER 1, which was the 1994 basic Krogh/Haussler behavior
rather than its actual power. (However, there's still a lot of bad
benchmarking, because people don't understand how to benchmark profile
software yet.)
Next: Plan 7
Up: Introduction
Previous: Profile HMMs
Direct comments and questions to <eddy@genetics.wustl.edu>